read_and_normalize450K: Normalization of 450K data by LOESS method
In normalize450K: Preprocessing of Illumina Infinium 450K data

Description Usage Arguments Details Value Note Author(s) References Examples

Read 450K '.idat' files and compute raw or normalized beta-values.

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read450K(idat_files)
normalize450K(intensities,tissue='')
dont_normalize450K(intensities)

`idat_files`	a character vector containing the paths to the .idat files stripped from the '_Grn.idat' suffix with one entry for each sample (.idat files for green and red intensities have to be in the same folder).
`intensities`	List object containing raw signal intensities. Result of calling `read450K`.
`tissue`	If set to 'Blood', a set of prespecified reference values are used for normalization. This is recommended if you plan to use `estimateLC`.

Function read450K reads .idat files and returns a list object containing raw signal intensities. dont_normalize450K returns an ExpressionSet containing beta-values without normalization. normalize450K performs dye bias correction using the extension controls probes followed by normalization by local regression (Heiss and Brenner, 2015) and returns an ExpressionSet containing beta-values, too.

For read450K a list containing the methylated, unmethylated and control signal intensities. For dont_normalize450K and normalize450K an ExpressionSet containing beta-values, rows corresponding to CpG sites (named) and columns to samples (in the same order as 'idat_files').

A benchmark comparing the performance of this method with other normalization approaches is provided in the vignette.

Jonathan A. Heiss

Heiss JA, Brenner H (2015). Between-array normalization for 450K data. Frontiers in Genetics, doi:10.3389/fgene.2015.00092

## Not run: 
 library(minfiData) ## this package includes some .idat files
 library(data.table)

 path <- system.file("extdata",package="minfiData")
 samples = fread(file.path(path, 'SampleSheet.csv'),integer64='character')

 samples[,file:=file.path(path,Sentrix_ID,paste0(Sentrix_ID,'_',Sentrix_Position))]
 ## samples$file is a character vector containing the location of the
 ## .idat files, but without the suffixes "_Red.idat" or "_Grn.idat"

 raw = read450K(samples$file)
 none = dont_normalize450K(raw) ## no normalization
 norm = normalize450K(raw)

## End(Not run)